[2024-01-25 19:43:35,435] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:35,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:35,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c61f660-c7d3-4442-a959-53f10a28ffbe/dqc_reference
[2024-01-25 19:43:36,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:36,540] [INFO] Task started: Prodigal
[2024-01-25 19:43:36,541] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc0e30cb-36e5-4458-99de-325199219047/GCF_014192415.1_ASM1419241v1_genomic.fna.gz | prodigal -d GCF_014192415.1_ASM1419241v1_genomic.fna/cds.fna -a GCF_014192415.1_ASM1419241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:45,548] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:45,549] [INFO] Task started: HMMsearch
[2024-01-25 19:43:45,549] [INFO] Running command: hmmsearch --tblout GCF_014192415.1_ASM1419241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c61f660-c7d3-4442-a959-53f10a28ffbe/dqc_reference/reference_markers.hmm GCF_014192415.1_ASM1419241v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:45,741] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:45,742] [INFO] Found 6/6 markers.
[2024-01-25 19:43:45,769] [INFO] Query marker FASTA was written to GCF_014192415.1_ASM1419241v1_genomic.fna/markers.fasta
[2024-01-25 19:43:45,769] [INFO] Task started: Blastn
[2024-01-25 19:43:45,769] [INFO] Running command: blastn -query GCF_014192415.1_ASM1419241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c61f660-c7d3-4442-a959-53f10a28ffbe/dqc_reference/reference_markers.fasta -out GCF_014192415.1_ASM1419241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:46,834] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:46,837] [INFO] Selected 15 target genomes.
[2024-01-25 19:43:46,837] [INFO] Target genome list was writen to GCF_014192415.1_ASM1419241v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:46,853] [INFO] Task started: fastANI
[2024-01-25 19:43:46,853] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc0e30cb-36e5-4458-99de-325199219047/GCF_014192415.1_ASM1419241v1_genomic.fna.gz --refList GCF_014192415.1_ASM1419241v1_genomic.fna/target_genomes.txt --output GCF_014192415.1_ASM1419241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:58,388] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:58,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c61f660-c7d3-4442-a959-53f10a28ffbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:58,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c61f660-c7d3-4442-a959-53f10a28ffbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:58,398] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:43:58,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:43:58,398] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Microbacterium proteolyticum	strain=CECT 8356	GCA_014192415.1	1572644	1572644	type	True	100.0	1156	1156	95	conclusive
Microbacterium enclense	strain=NIO-1002	GCA_900096885.1	993073	993073	type	True	86.9873	919	1156	95	below_threshold
Microbacterium enclense	strain=NIO-1002	GCA_001456955.1	993073	993073	type	True	86.9603	921	1156	95	below_threshold
Microbacterium testaceum	strain=NBRC 12675	GCA_006539145.1	2033	2033	suspected-type	True	85.028	821	1156	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	80.7363	570	1156	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	80.5976	533	1156	95	below_threshold
Microbacterium aurum	strain=DSM 8600	GCA_016907815.1	36805	36805	type	True	80.4197	495	1156	95	below_threshold
Microbacterium lushaniae	strain=L-031	GCA_008727775.1	2614639	2614639	type	True	80.3767	527	1156	95	below_threshold
Microbacterium hibisci	strain=CCTCC AB 2016180	GCA_015278255.1	2036000	2036000	type	True	80.3721	538	1156	95	below_threshold
Microbacterium sulfonylureivorans	strain=LAM7116	GCA_003999995.1	2486854	2486854	type	True	80.3648	536	1156	95	below_threshold
Microbacterium cremeum	strain=NY27	GCA_015277855.1	2782169	2782169	type	True	80.3611	544	1156	95	below_threshold
Microbacterium trichothecenolyticum	strain=DSM 8608	GCA_000956465.1	69370	69370	type	True	80.2177	581	1156	95	below_threshold
Microbacterium atlanticum	strain=WY121	GCA_015277815.1	2782168	2782168	type	True	80.1799	535	1156	95	below_threshold
Microbacterium hominis	strain=NBRC 15708	GCA_001592125.1	162426	162426	type	True	80.0654	529	1156	95	below_threshold
Microbacterium yannicii	strain=DSM 23203	GCA_024055635.1	671622	671622	type	True	79.9694	553	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:58,399] [INFO] DFAST Taxonomy check result was written to GCF_014192415.1_ASM1419241v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:58,400] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:58,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:58,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c61f660-c7d3-4442-a959-53f10a28ffbe/dqc_reference/checkm_data
[2024-01-25 19:43:58,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:58,438] [INFO] Task started: CheckM
[2024-01-25 19:43:58,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192415.1_ASM1419241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192415.1_ASM1419241v1_genomic.fna/checkm_input GCF_014192415.1_ASM1419241v1_genomic.fna/checkm_result
[2024-01-25 19:44:52,102] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:52,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:52,143] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:52,143] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:52,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192415.1_ASM1419241v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:52,146] [INFO] Task started: Blastn
[2024-01-25 19:44:52,146] [INFO] Running command: blastn -query GCF_014192415.1_ASM1419241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c61f660-c7d3-4442-a959-53f10a28ffbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192415.1_ASM1419241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:54,008] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:54,011] [INFO] Selected 18 target genomes.
[2024-01-25 19:44:54,011] [INFO] Target genome list was writen to GCF_014192415.1_ASM1419241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:54,025] [INFO] Task started: fastANI
[2024-01-25 19:44:54,025] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc0e30cb-36e5-4458-99de-325199219047/GCF_014192415.1_ASM1419241v1_genomic.fna.gz --refList GCF_014192415.1_ASM1419241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192415.1_ASM1419241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:09,289] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:09,301] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:09,301] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014192415.1	s__Microbacterium proteolyticum	100.0	1156	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001424225.1	s__Microbacterium sp001424225	91.9686	971	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001456955.1	s__Microbacterium enclense	86.9852	920	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.78	97.57	0.95	0.89	3	-
GCF_001792815.1	s__Microbacterium sp001792815	85.756	831	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.83	97.73	0.90	0.88	7	-
GCF_008763945.1	s__Microbacterium testaceum_G	85.6184	833	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679045.1	s__Microbacterium sp007679045	85.6177	808	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.00	99.00	0.94	0.94	2	-
GCF_900104345.1	s__Microbacterium testaceum_A	85.5586	803	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	97.34	95.96	0.91	0.90	3	-
GCF_900156435.1	s__Microbacterium sp900156435	85.5398	822	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003386675.1	s__Microbacterium chocolatum_A	85.1832	808	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.83	96.83	0.92	0.92	2	-
GCF_017833635.1	s__Microbacterium sp017833635	85.0841	808	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539145.1	s__Microbacterium testaceum	85.0248	821	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.70	98.67	0.94	0.93	3	-
GCF_000202635.1	s__Microbacterium testaceum_F	84.7165	813	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476285.1	s__Microbacterium testaceum_B	84.4841	753	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.43	98.38	0.88	0.88	4	-
GCF_005774735.1	s__Microbacterium sp005774735	83.7616	688	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.07	96.07	0.82	0.82	2	-
GCF_900156455.1	s__Microbacterium sp900156455	83.6331	760	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	96.72	96.66	0.88	0.87	4	-
GCF_001984105.1	s__Microbacterium sp001984105	83.4776	770	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.34	96.71	0.91	0.85	3	-
GCF_004366135.1	s__Microbacterium sp004366135	83.3316	728	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333395.1	s__Microbacterium sp000333395	83.1409	619	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:09,303] [INFO] GTDB search result was written to GCF_014192415.1_ASM1419241v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:09,303] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:09,306] [INFO] DFAST_QC result json was written to GCF_014192415.1_ASM1419241v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:09,307] [INFO] DFAST_QC completed!
[2024-01-25 19:45:09,307] [INFO] Total running time: 0h1m34s